travis clone depth

.travis.yml

@@ -4,6 +4,6 @@ rust:
   - beta
   - nightly
 git:
-  depth: 10
+  depth: 50
 after_success:
   ./.travis_bench.sh

Cargo.toml

@@ -4,6 +4,7 @@ version = "0.3.0"
 authors = ["Daniel Bauer <bauer@cbs.tu-darmstadt.de>"]
 license = "LGPL-3.0-only"
 edition = "2018"
+repository = "https://github.com/danijoo/xdrfile"
 description = "Wrapper around the gromacs libxdrfile library. Can be used to read and write gromacs trajectories in xtc and trr format."
 readme = "README.md"
 categories = ["external-ffi-bindings", "encoding", "science"]

README.md

@@ -1,4 +1,4 @@
-[![Build Status](https://travis-ci.com/danijoo/xdrfile.svg?branch=master)](https://travis-ci.com/danijoo/xdrfile) [![crates.io](https://img.shields.io/badge/crates.io-orange.svg?longCache=true)](https://www.crates.io/crates/xdrfile)
+[![Build Status](https://travis-ci.org/danijoo/xdrfile.svg?branch=master)](https://travis-ci.org/danijoo/xdrfile) [![crates.io](https://img.shields.io/badge/crates.io-orange.svg?longCache=true)](https://www.crates.io/crates/xdrfile) [![Latest Documentation](https://docs.rs/xdrfile/badge.svg)](https://docs.rs/xdrfile)
 
 # xdrfile
 Read and write xdr trajectory files in .xtc and .trr file format
@@ -29,7 +29,7 @@ fn main() -> Result<()> {
     assert_eq!(frame.step, 1);
     assert_eq!(frame.len(), num_atoms);
 
-    let first_atom_coords = frame.coords[0];
+    let first_atom_coords = frame[0];  // shorthand for frame.coords[0]
     assert_eq!(first_atom_coords, [-0.8901, 0.4127, -0.055499997]);
 
     Ok(())

src/errors.rs

@@ -64,7 +64,7 @@ impl std::error::Error for Error {
                 } else {
                     None
                 }
-            },
+            }
             Error::CouldNotCheckNAtoms(err) => Some(err.as_ref()),
             _ => None,
         }
@@ -200,7 +200,7 @@ pub enum ErrorCode {
 
 impl ErrorCode {
     /// True if the error is an end of file error, false otherwise
-    pub fn is_eof(&self) -> bool {
+    pub fn is_eof(self) -> bool {
         matches!(self, Self::ExdrEndOfFile)
     }
 }

src/frame.rs

@@ -1,3 +1,5 @@
+use std::ops::{Index, IndexMut};
+
 /// A frame represents a single step in a trajectory.
 #[derive(Clone, Debug)]
 pub struct Frame {
@@ -40,14 +42,13 @@ impl Frame {
     }
 
     /// Filters the frame by removing all atoms not matching the given indeces.
-    pub fn filter_coords(self: &mut Frame, indeces: &[usize]) {
+    pub fn filter_coords(self: &mut Frame, indices: &[usize]) {
         self.coords = self
             .coords
             .iter()
-            .map(|elem| elem.clone())
             .enumerate()
-            .filter(|&(i, _)| indeces.contains(&i))
-            .map(|(_, elem)| elem)
+            .filter(|(i, _)| indices.contains(i))
+            .map(|(_, elem)| *elem)
             .collect();
     }
 
@@ -67,6 +68,20 @@ impl Frame {
     }
 }
 
+impl Index<usize> for Frame {
+    type Output = [f32; 3];
+
+    fn index(&self, index: usize) -> &Self::Output {
+        &self.coords[index]
+    }
+}
+
+impl IndexMut<usize> for Frame {
+    fn index_mut(&mut self, index: usize) -> &mut Self::Output { {
+        &mut self.coords[index]
+    }}
+}
+
 #[cfg(test)]
 mod tests {
     use super::*;
@@ -81,15 +96,15 @@ mod tests {
     #[test]
     fn test_frame_filter_atoms() {
         let mut frame = Frame::with_len(3);
-        frame.coords[0] = [1.0, 2.0, 3.0];
-        frame.coords[1] = [4.0, 5.0, 6.0];
-        frame.coords[2] = [7.0, 8.0, 9.0];
+        frame[0] = [1.0, 2.0, 3.0];
+        frame[1] = [4.0, 5.0, 6.0];
+        frame[2] = [7.0, 8.0, 9.0];
         let filter: Vec<usize> = vec![1, 2];
         let mut frame_new = frame.clone();
         frame_new.filter_coords(&filter);
         assert!(frame_new.len() == filter.len());
-        assert!(frame_new.coords[0] == frame.coords[1]);
-        assert!(frame_new.coords[1] == frame.coords[2]);
+        assert!(frame_new.coords[0] == frame[1]);
+        assert!(frame_new.coords[1] == frame[2]);
     }
 
     #[test]
@@ -97,4 +112,60 @@ mod tests {
         let frame = Frame::with_len(10);
         assert_eq!(frame.len(), 10);
     }
+
+    #[test]
+    fn test_filter_coords() {
+        let mut frame = Frame {
+            step: 0,
+            time: 0.0,
+            box_vector: [[0.0; 3]; 3],
+            coords: vec![[0.0; 3], [1.0; 3], [2.0; 3]]
+        };
+
+        frame.filter_coords(&[1]);
+        for i in 0..3 {
+            assert_approx_eq!(frame[0][i], 1.0);
+        }
+    }
+
+    #[test]
+    #[allow(unused_mut)]
+    fn test_index() {
+        // test Index
+        let frame = Frame {
+            step: 0,
+            time: 0.0,
+            box_vector: [[0.0; 3]; 3],
+            coords: vec![[0.0; 3], [1.0; 3], [2.0; 3]]
+        };
+        for i in 0..frame.len() {
+            for j in 0..3 {
+                assert_approx_eq!(frame[i][j], frame[i][j]);
+            }
+        }
+
+        // test IndexMut
+        let mut frame = Frame {
+            step: 0,
+            time: 0.0,
+            box_vector: [[0.0; 3]; 3],
+            coords: vec![[0.0; 3], [1.0; 3], [2.0; 3]]
+        };
+        for i in 0..frame.len() {
+            for j in 0..3 {
+                assert_approx_eq!(frame[i][j], frame.coords[i][j]);
+            }
+        }
+
+        frame[0] = [123.0; 3];
+        for i in 0..frame.len() {
+            for j in 0..3 {
+                assert_approx_eq!(frame[i][j], frame.coords[i][j]);
+                if i == 0 {
+                    assert_approx_eq!(frame[i][j], 123.0);    
+                }
+            }
+        }
+
+    }
 }

src/iterator.rs

@@ -49,7 +49,7 @@ impl<T: Trajectory> TrajectoryIterator<T> {
         // It's OK to do this every frame because the result is cached by Trajectory
         let num_atoms = match &self.trajectory.get_num_atoms() {
             &Ok(n) => n,
-            Err(e) => Err(Error::CouldNotCheckNAtoms(Box::new(e.clone())))?,
+            Err(e) => return Err(Error::CouldNotCheckNAtoms(Box::new(e.clone()))),
         };
 
         // Reuse old frame

src/lib.rs

@@ -26,7 +26,7 @@
 //!     assert_eq!(frame.step, 1);
 //!     assert_eq!(frame.len(), num_atoms);
 //!
-//!     let first_atom_coords = frame.coords[0];
+//!     let first_atom_coords = frame[0];
 //!     assert_eq!(first_atom_coords, [-0.8901, 0.4127, -0.055499997]);
 //!
 //!     Ok(())
@@ -175,7 +175,7 @@ impl XDRFile {
                 })
             } else {
                 // Something went wrong. But the C api does not tell us what
-                Err((path, filemode))?
+                Err((path, filemode).into())
             }
         }
     }
@@ -232,6 +232,7 @@ pub trait Trajectory {
 
     /// Get the number of atoms from the give trajectory
     fn get_num_atoms(&mut self) -> Result<usize>;
+
 }
 
 /// Handle to Read/Write XTC Trajectories
@@ -275,8 +276,8 @@ impl Trajectory for XTCTrajectory {
             .get_num_atoms()
             .map_err(|e| Error::CouldNotCheckNAtoms(Box::new(e)))?;
         if num_atoms != frame.coords.len() {
-            Err((&*frame, num_atoms))?;
-        };
+            return Err((&*frame, num_atoms).into());
+        }
 
         unsafe {
             let code = xdrfile_xtc::read_xtc(
@@ -402,7 +403,7 @@ impl Trajectory for TRRTrajectory {
             .get_num_atoms()
             .map_err(|e| Error::CouldNotCheckNAtoms(Box::new(e)))?;
         if num_atoms != frame.coords.len() {
-            Err((&*frame, num_atoms))?;
+            return Err((&*frame, num_atoms).into());
         }
 
         unsafe {
@@ -501,14 +502,15 @@ mod tests {
     use tempfile::NamedTempFile;
 
     #[test]
-    fn test_read_write_xtc() -> Result<()> {
+    fn test_write_append_read_xtc() -> Result<()> {
         let tempfile = NamedTempFile::new().expect("Could not create temporary file");
         let tmp_path = tempfile.path();
-
         let natoms = 2;
+
+        // write frame 1
         let frame = Frame {
-            step: 5,
-            time: 2.0,
+            step: 1,
+            time: 1.0,
             box_vector: [[1.0, 2.0, 3.0], [2.0, 1.0, 3.0], [3.0, 2.0, 1.0]],
             coords: vec![[1.0, 1.0, 1.0], [1.0, 1.0, 1.0]],
         };
@@ -520,11 +522,28 @@ mod tests {
         }
         f.flush()?;
 
+        // append frame 2
+        let frame2 = Frame {
+            step: 2,
+            time: 2.0,
+            box_vector: [[1.0, 2.0, 3.0], [2.0, 1.0, 3.0], [3.0, 2.0, 1.0]],
+            coords: vec![[1.0, 1.0, 1.0], [1.0, 1.0, 1.0]],
+        };
+        let mut f = XTCTrajectory::open_append(&tmp_path)?;
+        let write_status = f.write(&frame2);
+        match write_status {
+            Err(_) => panic!("Failed"),
+            Ok(()) => {}
+        }
+        f.flush()?;
+
+        // open trj for read
         let mut new_frame = Frame::with_len(natoms);
         let mut f = XTCTrajectory::open_read(tmp_path)?;
         let num_atoms = f.get_num_atoms()?;
         assert_eq!(num_atoms, natoms);
 
+        // check frame 1 ...
         let read_status = f.read(&mut new_frame);
         match read_status {
             Err(e) => assert!(false, "{:?}", e),
@@ -536,22 +555,36 @@ mod tests {
         assert_approx_eq!(new_frame.time, frame.time);
         assert_eq!(new_frame.box_vector, frame.box_vector);
         assert_eq!(new_frame.coords, frame.coords);
+
+        // and check frame 1 ...
+        let read_status = f.read(&mut new_frame);
+        match read_status {
+            Err(e) => assert!(false, "{:?}", e),
+            Ok(()) => {}
+        }
+
+        assert_eq!(new_frame.len(), frame2.len());
+        assert_eq!(new_frame.step, frame2.step);
+        assert_approx_eq!(new_frame.time, frame2.time);
+        assert_eq!(new_frame.box_vector, frame2.box_vector);
+        assert_eq!(new_frame.coords, frame2.coords);
         Ok(())
     }
 
     #[test]
-    fn test_read_write_trr() -> Result<()> {
+    fn test_write_append_read_trr() -> Result<()> {
         let tempfile = NamedTempFile::new().expect("Could not create temporary file");
         let tmp_path = tempfile.path();
-
         let natoms = 2;
+
+        // write frame 1
         let frame = Frame {
-            step: 5,
-            time: 2.0,
+            step: 1,
+            time: 1.0,
             box_vector: [[1.0, 2.0, 3.0], [2.0, 1.0, 3.0], [3.0, 2.0, 1.0]],
             coords: vec![[1.0, 1.0, 1.0], [1.0, 1.0, 1.0]],
         };
-        let mut f = TRRTrajectory::open_write(tmp_path)?;
+        let mut f = TRRTrajectory::open_write(&tmp_path)?;
         let write_status = f.write(&frame);
         match write_status {
             Err(_) => panic!("Failed"),
@@ -559,11 +592,28 @@ mod tests {
         }
         f.flush()?;
 
+        // append frame 2
+        let frame2 = Frame {
+            step: 2,
+            time: 2.0,
+            box_vector: [[1.0, 2.0, 3.0], [2.0, 1.0, 3.0], [3.0, 2.0, 1.0]],
+            coords: vec![[1.0, 1.0, 1.0], [1.0, 1.0, 1.0]],
+        };
+        let mut f = TRRTrajectory::open_append(&tmp_path)?;
+        let write_status = f.write(&frame2);
+        match write_status {
+            Err(_) => panic!("Failed"),
+            Ok(()) => {}
+        }
+        f.flush()?;
+
+        // open trj for read
         let mut new_frame = Frame::with_len(natoms);
         let mut f = TRRTrajectory::open_read(tmp_path)?;
-        // let num_atoms = f.get_num_atoms()?;
-        // assert_eq!(num_atoms, natoms);
+        let num_atoms = f.get_num_atoms()?;
+        assert_eq!(num_atoms, natoms);
 
+        // check frame 1 ...
         let read_status = f.read(&mut new_frame);
         match read_status {
             Err(e) => assert!(false, "{:?}", e),
@@ -572,9 +622,22 @@ mod tests {
 
         assert_eq!(new_frame.len(), frame.len());
         assert_eq!(new_frame.step, frame.step);
-        assert_eq!(new_frame.time, frame.time);
+        assert_approx_eq!(new_frame.time, frame.time);
         assert_eq!(new_frame.box_vector, frame.box_vector);
         assert_eq!(new_frame.coords, frame.coords);
+
+        // and check frame 1 ...
+        let read_status = f.read(&mut new_frame);
+        match read_status {
+            Err(e) => assert!(false, "{:?}", e),
+            Ok(()) => {}
+        }
+
+        assert_eq!(new_frame.len(), frame2.len());
+        assert_eq!(new_frame.step, frame2.step);
+        assert_approx_eq!(new_frame.time, frame2.time);
+        assert_eq!(new_frame.box_vector, frame2.box_vector);
+        assert_eq!(new_frame.coords, frame2.coords);
         Ok(())
     }
 
@@ -631,21 +694,17 @@ mod tests {
             Ok(s) => {
                 assert_eq!(s, CString::new("test")?);
             }
-            Err(_) => panic!("Valid Path failed to convert to CString.")
+            Err(_) => panic!("Valid Path failed to convert to CString."),
         }
 
         // \0 in path should result in an InvalidOsStr(Some(NulError))
         let result = path_to_cstring(PathBuf::from("invalid/\0path"));
         match result {
             Ok(_) => panic!("Cstring conversion did not fail"),
-            Err(e) => {
-                match e {
-                    Error::InvalidOsStr(opt) => {
-                        assert!(opt.is_some())
-                    }
-                    _ => panic!("Wrong error type. (This should never happend).")
-                }
-            }
+            Err(e) => match e {
+                Error::InvalidOsStr(opt) => assert!(opt.is_some()),
+                _ => panic!("Wrong error type. (This should never happend)."),
+            },
         }
         Ok(())
     }